Estimating IBD tracts from low coverage NGS data - PubMed (original) (raw)
. 2016 Jul 15;32(14):2096-102.
doi: 10.1093/bioinformatics/btw212. Epub 2016 Apr 22.
Affiliations
- PMID: 27153648
- DOI: 10.1093/bioinformatics/btw212
Estimating IBD tracts from low coverage NGS data
Filipe G Vieira et al. Bioinformatics. 2016.
Abstract
Motivation: The amount of IBD in an individual depends on the relatedness of the individual's parents. However, it can also provide information regarding mating system, past history and effective size of the population from which the individual has been sampled.
Results: Here, we present a new method for estimating inbreeding IBD tracts from low coverage NGS data. Contrary to other methods that use genotype data, the one presented here uses genotype likelihoods to take the uncertainty of the data into account. We benchmark it under a wide range of biologically relevant conditions and show that the new method provides a marked increase in accuracy even at low coverage.
Availability and implementation: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM CONTACT: fgvieira@snm.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Similar articles
- SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data.
Blischak PD, Kubatko LS, Wolfe AD. Blischak PD, et al. Bioinformatics. 2018 Feb 1;34(3):407-415. doi: 10.1093/bioinformatics/btx587. Bioinformatics. 2018. PMID: 29028881 - NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data.
Korneliussen TS, Moltke I. Korneliussen TS, et al. Bioinformatics. 2015 Dec 15;31(24):4009-11. doi: 10.1093/bioinformatics/btv509. Epub 2015 Aug 30. Bioinformatics. 2015. PMID: 26323718 Free PMC article. - LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
Severson AL, Korneliussen TS, Moltke I. Severson AL, et al. Bioinformatics. 2022 Jan 27;38(4):1159-1161. doi: 10.1093/bioinformatics/btab732. Bioinformatics. 2022. PMID: 34718411 Free PMC article. - ngsLD: evaluating linkage disequilibrium using genotype likelihoods.
Fox EA, Wright AE, Fumagalli M, Vieira FG. Fox EA, et al. Bioinformatics. 2019 Oct 1;35(19):3855-3856. doi: 10.1093/bioinformatics/btz200. Bioinformatics. 2019. PMID: 30903149 - fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample.
Jørsboe E, Hanghøj K, Albrechtsen A. Jørsboe E, et al. Bioinformatics. 2017 Oct 1;33(19):3148-3150. doi: 10.1093/bioinformatics/btx474. Bioinformatics. 2017. PMID: 28957500
Cited by
- A new method for ecologists to estimate heterozygote excess and deficit for multi-locus gene families.
O'Reilly GD, Manlik O, Vardeh S, Sinclair J, Cannell B, Lawler ZP, Sherwin WB. O'Reilly GD, et al. Ecol Evol. 2024 Jul 23;14(7):e11561. doi: 10.1002/ece3.11561. eCollection 2024 Jul. Ecol Evol. 2024. PMID: 39045501 Free PMC article. - Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.
Naji MM, Gualdrón Duarte JL, Forneris NS, Druet T. Naji MM, et al. Genet Sel Evol. 2024 Jan 31;56(1):10. doi: 10.1186/s12711-024-00878-7. Genet Sel Evol. 2024. PMID: 38297209 Free PMC article. - Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict.
Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. Talavera A, et al. iScience. 2023 Dec 12;27(1):108665. doi: 10.1016/j.isci.2023.108665. eCollection 2024 Jan 19. iScience. 2023. PMID: 38226169 Free PMC article. - Accurate detection of identity-by-descent segments in human ancient DNA.
Ringbauer H, Huang Y, Akbari A, Mallick S, Olalde I, Patterson N, Reich D. Ringbauer H, et al. Nat Genet. 2024 Jan;56(1):143-151. doi: 10.1038/s41588-023-01582-w. Epub 2023 Dec 20. Nat Genet. 2024. PMID: 38123640 Free PMC article. - Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer.
Burnett HA, Bieker VC, Le Moullec M, Peeters B, Rosvold J, Pedersen ÅØ, Dalén L, Loe LE, Jensen H, Hansen BB, Martin MD. Burnett HA, et al. Evol Appl. 2023 Aug 22;16(9):1531-1548. doi: 10.1111/eva.13585. eCollection 2023 Sep. Evol Appl. 2023. PMID: 37752961 Free PMC article.
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous